3QIL | pdb_00003qil

Crystal structure analysis of the clathrin trimerization domain

PDB DOI: https://doi.org/10.2210/pdb3QIL/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Bos taurus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-01-27 Released: 2012-02-01
Deposition Author(s): Ybe, J.A., Mishra, S., Nix, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free:
0.386 (Depositor), 0.352 (DCC)
R-Value Work:
0.339 (Depositor), 0.341 (DCC)
R-Value Observed:
0.339 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3QIL

This is version 1.3 of the entry. See complete history.

Literature

Nuclear localization of clathrin involves a labile helix outside the trimerization domain.

Ybe, J.A., Fontaine, S.N., Stone, T., Nix, J., Lin, X., Mishra, S.

(2013) FEBS Lett 587: 142-149

PubMed: 23178717 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.febslet.2012.11.005
Primary Citation Related Structures:
3QIL

PubMed Abstract:
Clathrin is a trimeric protein involved in receptor-mediated-endocytosis, but can function as a non-trimer outside of endocytosis. We have discovered that the subcellular distribution of a clathrin cysteine mutant we previously studied is altered and a proportion is also localized to nuclear spaces. MALS shows C1573A hub is a mixture of trimer-like and detrimerized molecules. The X-ray structure of the trimerization domain reveals that without light chains, a helix harboring cysteine-1573 is reoriented. We propose clathrin has a detrimerization switch, which suggests clathrin topology can be altered naturally for new functions.

Organizational Affiliation

Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA. jybe@indiana.edu

Macromolecule Content

Total Structure Weight: 354.21 kDa
Atom Count: 23,032
Modeled Residue Count: 2,776
Deposited Residue Count: 3,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clathrin heavy chain 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	125	Bos taurus	Mutation(s): 2 Gene Names: CLTC
UniProt
Find proteins for P49951 (Bos taurus) Explore P49951 Go to UniProtKB: P49951
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49951
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free: 0.386 (Depositor), 0.352 (DCC)
R-Value Work: 0.339 (Depositor), 0.341 (DCC)
R-Value Observed: 0.339 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.78	α = 90
b = 255.78	β = 90
c = 312.99	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2013-01-16
Changes: Database references
Version 1.2: 2013-06-19
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.